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Commit d829626f by peastman
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Merge pull request #132 from peastman/duplicates 

Removed duplicate templates from soft.xml
parents fb8eea15 dbc01eab
Showing with 3 additions and 271 deletions
pdbfixer/soft.xml
......@@ -1747,27 +1747,6 @@
<Bond from="6" to="7"/>
<ExternalBond from="6"/>
</Residue>
<Residue name="LYN">
<Atom name="N" type="214"/>
<Atom name="CA" type="216"/>
<Atom name="CB" type="218"/>
<Atom name="CG" type="220"/>
<Atom name="CD" type="222"/>
<Atom name="CE" type="224"/>
<Atom name="NZ" type="226"/>
<Atom name="C" type="228"/>
<Atom name="O" type="229"/>
<Bond from="0" to="1"/>
<Bond from="1" to="2"/>
<Bond from="1" to="7"/>
<Bond from="2" to="3"/>
<Bond from="3" to="4"/>
<Bond from="4" to="5"/>
<Bond from="5" to="6"/>
<Bond from="7" to="8"/>
<ExternalBond from="0"/>
<ExternalBond from="7"/>
</Residue>
<Residue name="NGLY">
<Atom name="N" type="810"/>
<Atom name="CA" type="812"/>
......@@ -2087,21 +2066,6 @@
<Bond from="4" to="5"/>
<ExternalBond from="4"/>
</Residue>
<Residue name="NCYX">
<Atom name="N" type="774"/>
<Atom name="CA" type="776"/>
<Atom name="CB" type="778"/>
<Atom name="SG" type="780"/>
<Atom name="C" type="781"/>
<Atom name="O" type="782"/>
<Bond from="0" to="1"/>
<Bond from="1" to="2"/>
<Bond from="1" to="4"/>
<Bond from="2" to="3"/>
<Bond from="4" to="5"/>
<ExternalBond from="4"/>
<ExternalBond from="3"/>
</Residue>
<Residue name="TYR">
<Atom name="N" type="334"/>
<Atom name="CA" type="336"/>
......@@ -2210,30 +2174,7 @@
<Bond from="9" to="11"/>
<ExternalBond from="0"/>
</Residue>
<Residue name="NHIE">
<Atom name="N" type="832"/>
<Atom name="CA" type="834"/>
<Atom name="CB" type="836"/>
<Atom name="CG" type="838"/>
<Atom name="ND1" type="839"/>
<Atom name="CE1" type="840"/>
<Atom name="NE2" type="842"/>
<Atom name="CD2" type="844"/>
<Atom name="C" type="846"/>
<Atom name="O" type="847"/>
<Bond from="0" to="1"/>
<Bond from="1" to="2"/>
<Bond from="1" to="8"/>
<Bond from="2" to="3"/>
<Bond from="3" to="4"/>
<Bond from="3" to="7"/>
<Bond from="4" to="5"/>
<Bond from="5" to="6"/>
<Bond from="6" to="7"/>
<Bond from="8" to="9"/>
<ExternalBond from="8"/>
</Residue>
<Residue name="NHID">
<Residue name="NHIS">
<Atom name="N" type="816"/>
<Atom name="CA" type="818"/>
<Atom name="CB" type="820"/>
......@@ -2283,29 +2224,6 @@
<Bond from="7" to="8"/>
<ExternalBond from="7"/>
</Residue>
<Residue name="NHIP">
<Atom name="N" type="848"/>
<Atom name="CA" type="850"/>
<Atom name="CB" type="852"/>
<Atom name="CG" type="854"/>
<Atom name="ND1" type="855"/>
<Atom name="CE1" type="857"/>
<Atom name="NE2" type="859"/>
<Atom name="CD2" type="861"/>
<Atom name="C" type="863"/>
<Atom name="O" type="864"/>
<Bond from="0" to="1"/>
<Bond from="1" to="2"/>
<Bond from="1" to="8"/>
<Bond from="2" to="3"/>
<Bond from="3" to="4"/>
<Bond from="3" to="7"/>
<Bond from="4" to="5"/>
<Bond from="5" to="6"/>
<Bond from="6" to="7"/>
<Bond from="8" to="9"/>
<ExternalBond from="8"/>
</Residue>
<Residue name="RGN">
<Atom name="O5'" type="1810"/>
<Atom name="C5'" type="1811"/>
......@@ -2803,27 +2721,6 @@
<Bond from="14" to="16"/>
<ExternalBond from="16"/>
</Residue>
<Residue name="GLH">
<Atom name="N" type="90"/>
<Atom name="CA" type="92"/>
<Atom name="CB" type="94"/>
<Atom name="CG" type="96"/>
<Atom name="CD" type="98"/>
<Atom name="OE1" type="99"/>
<Atom name="OE2" type="100"/>
<Atom name="C" type="102"/>
<Atom name="O" type="103"/>
<Bond from="0" to="1"/>
<Bond from="1" to="2"/>
<Bond from="1" to="7"/>
<Bond from="2" to="3"/>
<Bond from="3" to="4"/>
<Bond from="4" to="5"/>
<Bond from="4" to="6"/>
<Bond from="7" to="8"/>
<ExternalBond from="0"/>
<ExternalBond from="7"/>
</Residue>
<Residue name="ILE">
<Atom name="N" type="186"/>
<Atom name="CA" type="188"/>
......@@ -2854,31 +2751,6 @@
<Residue name="K+">
<Atom name="K+" type="1956"/>
</Residue>
<Residue name="CHIP">
<Atom name="N" type="511"/>
<Atom name="CA" type="513"/>
<Atom name="CB" type="515"/>
<Atom name="CG" type="517"/>
<Atom name="ND1" type="518"/>
<Atom name="CE1" type="520"/>
<Atom name="NE2" type="522"/>
<Atom name="CD2" type="524"/>
<Atom name="C" type="526"/>
<Atom name="O" type="527"/>
<Atom name="OXT" type="528"/>
<Bond from="0" to="1"/>
<Bond from="1" to="2"/>
<Bond from="1" to="8"/>
<Bond from="2" to="3"/>
<Bond from="3" to="4"/>
<Bond from="3" to="7"/>
<Bond from="4" to="5"/>
<Bond from="5" to="6"/>
<Bond from="6" to="7"/>
<Bond from="8" to="9"/>
<Bond from="8" to="10"/>
<ExternalBond from="0"/>
</Residue>
<Residue name="GLY">
<Atom name="N" type="131"/>
<Atom name="CA" type="133"/>
......@@ -2958,7 +2830,7 @@
<ExternalBond from="0"/>
<ExternalBond from="7"/>
</Residue>
<Residue name="CHID">
<Residue name="CHIS">
<Atom name="N" type="477"/>
<Atom name="CA" type="479"/>
<Atom name="CB" type="481"/>
......@@ -2983,31 +2855,6 @@
<Bond from="8" to="10"/>
<ExternalBond from="0"/>
</Residue>
<Residue name="CHIE">
<Atom name="N" type="494"/>
<Atom name="CA" type="496"/>
<Atom name="CB" type="498"/>
<Atom name="CG" type="500"/>
<Atom name="ND1" type="501"/>
<Atom name="CE1" type="502"/>
<Atom name="NE2" type="504"/>
<Atom name="CD2" type="506"/>
<Atom name="C" type="508"/>
<Atom name="O" type="509"/>
<Atom name="OXT" type="510"/>
<Bond from="0" to="1"/>
<Bond from="1" to="2"/>
<Bond from="1" to="8"/>
<Bond from="2" to="3"/>
<Bond from="3" to="4"/>
<Bond from="3" to="7"/>
<Bond from="4" to="5"/>
<Bond from="5" to="6"/>
<Bond from="6" to="7"/>
<Bond from="8" to="9"/>
<Bond from="8" to="10"/>
<ExternalBond from="0"/>
</Residue>
<Residue name="NALA">
<Atom name="N" type="714"/>
<Atom name="CA" type="716"/>
......@@ -3186,25 +3033,6 @@
<ExternalBond from="0"/>
<ExternalBond from="21"/>
</Residue>
<Residue name="ASH">
<Atom name="N" type="27"/>
<Atom name="CA" type="29"/>
<Atom name="CB" type="31"/>
<Atom name="CG" type="33"/>
<Atom name="OD1" type="34"/>
<Atom name="OD2" type="35"/>
<Atom name="C" type="37"/>
<Atom name="O" type="38"/>
<Bond from="0" to="1"/>
<Bond from="1" to="2"/>
<Bond from="1" to="6"/>
<Bond from="2" to="3"/>
<Bond from="3" to="4"/>
<Bond from="3" to="5"/>
<Bond from="6" to="7"/>
<ExternalBond from="0"/>
<ExternalBond from="6"/>
</Residue>
<Residue name="ASN">
<Atom name="N" type="39"/>
<Atom name="CA" type="41"/>
......@@ -3527,23 +3355,6 @@
<Bond from="4" to="6"/>
<ExternalBond from="0"/>
</Residue>
<Residue name="CCYX">
<Atom name="N" type="431"/>
<Atom name="CA" type="433"/>
<Atom name="CB" type="435"/>
<Atom name="SG" type="437"/>
<Atom name="C" type="438"/>
<Atom name="O" type="439"/>
<Atom name="OXT" type="440"/>
<Bond from="0" to="1"/>
<Bond from="1" to="2"/>
<Bond from="1" to="4"/>
<Bond from="2" to="3"/>
<Bond from="4" to="5"/>
<Bond from="4" to="6"/>
<ExternalBond from="0"/>
<ExternalBond from="3"/>
</Residue>
<Residue name="CMET">
<Atom name="N" type="576"/>
<Atom name="CA" type="578"/>
......@@ -3755,30 +3566,6 @@
<Bond from="5" to="7"/>
<ExternalBond from="0"/>
</Residue>
<Residue name="HIP">
<Atom name="N" type="169"/>
<Atom name="CA" type="171"/>
<Atom name="CB" type="173"/>
<Atom name="CG" type="175"/>
<Atom name="ND1" type="176"/>
<Atom name="CE1" type="178"/>
<Atom name="NE2" type="180"/>
<Atom name="CD2" type="182"/>
<Atom name="C" type="184"/>
<Atom name="O" type="185"/>
<Bond from="0" to="1"/>
<Bond from="1" to="2"/>
<Bond from="1" to="8"/>
<Bond from="2" to="3"/>
<Bond from="3" to="4"/>
<Bond from="3" to="7"/>
<Bond from="4" to="5"/>
<Bond from="5" to="6"/>
<Bond from="6" to="7"/>
<Bond from="8" to="9"/>
<ExternalBond from="0"/>
<ExternalBond from="8"/>
</Residue>
<Residue name="DAN">
<Atom name="O5'" type="1117"/>
<Atom name="C5'" type="1118"/>
......@@ -3819,23 +3606,7 @@
<Bond from="15" to="16"/>
<Bond from="15" to="17"/>
</Residue>
<Residue name="CYX">
<Atom name="N" type="81"/>
<Atom name="CA" type="83"/>
<Atom name="CB" type="85"/>
<Atom name="SG" type="87"/>
<Atom name="C" type="88"/>
<Atom name="O" type="89"/>
<Bond from="0" to="1"/>
<Bond from="1" to="2"/>
<Bond from="1" to="4"/>
<Bond from="2" to="3"/>
<Bond from="4" to="5"/>
<ExternalBond from="0"/>
<ExternalBond from="4"/>
<ExternalBond from="3"/>
</Residue>
<Residue name="HID">
<Residue name="HIS">
<Atom name="N" type="137"/>
<Atom name="CA" type="139"/>
<Atom name="CB" type="141"/>
......@@ -3859,45 +3630,6 @@
<ExternalBond from="0"/>
<ExternalBond from="8"/>
</Residue>
<Residue name="HIE">
<Atom name="N" type="153"/>
<Atom name="CA" type="155"/>
<Atom name="CB" type="157"/>
<Atom name="CG" type="159"/>
<Atom name="ND1" type="160"/>
<Atom name="CE1" type="161"/>
<Atom name="NE2" type="163"/>
<Atom name="CD2" type="165"/>
<Atom name="C" type="167"/>
<Atom name="O" type="168"/>
<Bond from="0" to="1"/>
<Bond from="1" to="2"/>
<Bond from="1" to="8"/>
<Bond from="2" to="3"/>
<Bond from="3" to="4"/>
<Bond from="3" to="7"/>
<Bond from="4" to="5"/>
<Bond from="5" to="6"/>
<Bond from="6" to="7"/>
<Bond from="8" to="9"/>
<ExternalBond from="0"/>
<ExternalBond from="8"/>
</Residue>
<Residue name="CYM">
<Atom name="N" type="62"/>
<Atom name="CA" type="64"/>
<Atom name="CB" type="66"/>
<Atom name="SG" type="68"/>
<Atom name="C" type="69"/>
<Atom name="O" type="70"/>
<Bond from="0" to="1"/>
<Bond from="1" to="2"/>
<Bond from="1" to="4"/>
<Bond from="2" to="3"/>
<Bond from="4" to="5"/>
<ExternalBond from="0"/>
<ExternalBond from="4"/>
</Residue>
<Residue name="CYS">
<Atom name="N" type="71"/>
<Atom name="CA" type="73"/>
......
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